Dear all,
I have run cmsearch from infernal 1.1 to annotate non-coding RNAs in my genome of interest.
With the option --tblout I...
17 results in 0.0028 seconds.
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converting infernal -tblout output to gff
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Can't sort BAM file ("not a BAM file")
Dear everyone,
I try to convert some SAM files to BAM files following the Samtools FAQ method :
First indexing my reference fasta... -
How to convert sam/bam or bed file into wig file
Hi,
How what tools can I use to convert sam/bam or bed file into a wig file? -
Consensus fastq to VCF
Hello,
I'm looking for a tool to undo the vcf2fq operation performed by vcfutils.pl in the samtools package.
I have a bunch... -
Convert pileup to bed
Hello,
I'm currently using samtools mpileup like this:
...Code:samtools mpileup -l target_regions.bed file1.bam file2.bam file3.bam
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How to convert to or get 1000 Genomes phase1 data mapped to hg18.
Hello.
I'm trying to annotate my variant data with 1000 genomes phase1 data.
(ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.vcf)... -
Converting a fixed step wiggle file to a bigWig.
I have a fixed step wiggle file which I'm trying to convert to a bigWig file but I'm not getting anywhere. Here are the first few lines of the fixed step... -
Convert Cytogenetic location to base pair position
Hi everybody.
I am trying to collect annotation files so that I can annotate as many of my variants as possible with functional elements. I am... -
convert plink files to VCF
Hi,
I would like to know if anyone has a script/tool to convert plink .map and .ped files into VCF.
We should have in mind... -
Convert merged BAM back to per lane BAM or FASTQ file
I have got some illumina data in a a merged BAM file for a particular sample and I would like to convert it back to per lane data files (BAM or fastq)... -
Convert SOAPsplice v1.4 output to SAM
Hi all, I'm trying to use SOAPsplice 1.4 to align some paired end reads. The alignment works fine, but the output is a custom format. Does anyone know... -
strand specific wig files
Hi,
I am trying to create strand-specific wig files from a bam file.
I used the pileup option and i thought it worked very good.... -
help on "truncated file", when converting sam to bam
When I convert my sam file to bam file, I got "truncated file" in prompt, and also "[sam_read1] reference '503821040998320619' is ecognized... -
how to convert sam to bam with EOF marker in header
I aligned short reads by an nonpublished aligner. Then I converted the
alignments to sam, then bam, and sote bam. It looks they worked for
... -
Convert from baf to bam files
Hi everyone,
I'm trying to convert my baf files to bam, because i want to use dindel.
So i use bfast to convert from baf...
